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Many researchers lack a 'nuts-and-bolts' appreciation of the different types of microarray and their manufacture and processing. A detailed and thorough understanding of the options available improves the odds that one's choice will be vindicated; an appreciation of the biological context of genetic (and genomic) questions can also be critical to the success of microarray analysis. The articles in this special supplement of Nature Genetics have been selected with these issues in mind. The limitations and the ultimate utility of the microarray remain to be determined, however, as pointed out in the Foreword by Francis Collins of the National Human Genome Research Institute (NHGRI) – the generous sponsor of this supplement. It is hoped that in addition to serving as a practical resource, the contents of this supplement will provide a glimpse of things to come.